From: jz7_at_duke.edu
Date: Wed Jun 02 2004 - 16:13:14 CDT
Thanks!
I have parm*.dat file. But first, how to generate the psf structure file?
The way I did in Charmm ff is write a tcl file, which specify the topology
file and the gragments. But when using Amber, what command lines should I
add? What is the corresponding topology file? (Is it the ".inp" file in
Amber force field? But it has seperate file for protein and DNA. How can I
include both of them?)
Thanks a lot!
Best,
Jeny
On Wed, 2 Jun 2004, Brian Bennion wrote:
>
> Hello Jeny,
>
> What part of this page has you stuck?
>
> http://www.ks.uiuc.edu/Research/namd/current/ug/node15.html
>
> if you are needing to use the amber functions of NAMD then you must have a
> an amber parm file laying around. This rest is as stated on the above web
> page.
>
> Brian
>
>
> On Wed, 2 Jun 2004 jz7_at_duke.edu wrote:
>
> > Dear all,
> >
> > I am trying to use Amber force field in NAMD. After reading the User's
> > manual, I am still not quite clear about how to do that. So I am
> > wondering if there are some sample inputs for generating PSF file,
> > minimization, etc. I have some experience on using NAMD with Charmm
> > force field. What's the difference between using Amber and using Charmm
> > in NAMD?
> >
> > Thanks a lot!
> >
> > Sincerely,
> > Jeny
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>
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